To answer your question...it's unlikely that the type of connector on your cable will effect the output of your amp.
Now...some amps will have both the 1/4" and speakon outputs, it's been my experience that the 1/4" is used if you're running in stereo, and the speakon is used if in mono, not all amps are setup or wired this way, but most that I have run across are. What I use in this situation (to run mono and most wattage), is a cable with speakon on one end and 1/4" on the other.
The basic electrical difference between the 2 technologies as I understand it, is about the same as using a polorized (2 prong) plug compared to a grounded (3 prong) plug. So, instead of using a simple Tip and ring configuration, you're using what's called a tip, ring, and sleeve (tip is grounded conductor, ring is power, and sleeve is grounding conductor).
Maybe that helps...maybe I'm completely nuts or wrong in this scenario. Best advice would be to read the manual for your amp.